Mission: Iconic Reefs and National Coral Reef Monitoring Program Benthic Analysis

Summary Report for 2022 and 2024

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Mission Iconic Reef Logo
Authors:
Nicole Krampitz1, Julia Mateski1, Dione Swanson2,3
1 CSS, Inc. under contract to NOAA National Ocean Service, National Centers for Coastal Ocean Science
2 NOAA National Marine Fisheries Service, Southeast Fisheries Science Center
3 University of Miami, Cooperative Institute for Marine and Atmospheric Studies

1 Introduction

Mission: Iconic Reefs (M:IR) is a multi-institutional initiative designed to restore ecological function and biodiversity across key reef sites in the Florida Keys. Led by NOAA in collaboration with federal, state, institutional, and non-profit partners, M:IR targets nearly three million square feet of reef at seven key coral reefs in the Florida Keys National Marine Sanctuary (FKNMS). The overarching M:IR goal is to restore coral cover and reef function to a self-sustaining state.  

Monitoring the response of coral reef benthic communities and coral populations to reef restoration is essential to quantify changes over time from restoration (Goergen et al. 2022). For this comparison of the status of Iconic Reefs in comparison to Florida Keys reefs, National Coral Reef Monitoring Program (NCRMP) surveys were conducted in 2022 and 2024 by the FKNMS M:IR field team. NCRMP surveys are conducted on shallow (<30 m), hard-bottom reef habitats and employ a stratified-random, one-stage design within 50 m × 50 m grid cells to ensure representative sampling across depth and rugosity strata (Ault et al., 2021). The NCRMP survey design ensures that survey sites are allocated by cross-shelf zone, rugosity type, and depth strata with sites distributed around the Florida Keys from nearshore to offshore to a maximum depth of 30 m.  The NCRMP sample grid was spatially joined with the seven distinct MIR zones (Figure 1): Carysfort (North and South), Cheeca Rocks, Eastern Dry Rocks, Horseshoe Reef, Looe Key, Newfound Harbor, and Sombrero Reef. Survey sites were proportionally allocated within NCRMP strata to maintain consistent representation across habitats. 

Figure 1: Map of the Florida Keys showing the sites of Mission:Iconic Reefs

Corals and benthic communities were monitored using two different NCRMP surveys: the Benthic Community Assessment survey and the Coral Demographics survey (NOAA CRCP 2022a, 2022b, 2024a, 2024b). The Benthic Community Assessment survey includes: 1) benthic cover (%) estimates along a 15-m transect with a line point intercept method, 2) presence/absence of Endangered Species Act (ESA)-listed coral species (NOAA National Marine Fisheries Service, 2014), 3) abundance of key macroinvertebrates, and 4) reef rugosity measurements within a 15 m x 2 m belt-transect area (NOAA CRCP 2022a, 2024b). At the same site, coral demographics were surveyed within a 10 m x 1 m belt-transect area (NOAA CRCP 2022b, 2024b). NCRMP coral demographic survey data were combined with complementarily allocated survey data from Florida Fish and Wildlife Conservation Commission’s Disturbance Response Monitoring (DRM). In all coral demographics surveys, all live coral colonies ≧ 4 cm were counted, identified to species, measured to the nearest centimeter, and estimates were made of the proportion per colony of any present mortality (recent or old), disease (absent, present: slow, fast), and/or bleaching (none, total, partial, paling). Only live coral colonies were included in the survey; dead colonies with 100% mortality were not surveyed (e.g., colonies killed by coral disease). Juvenile corals (< 4 cm) were reported for species richness only and were not included in counts, size measurements, or estimates of condition (NOAA CRCP 2022b); in 2024, juveniles of select coral species were counted (NOAA CRCP 2024b). In 2024, NCRMP benthic surveys also included large area imaging (LAI) collected at most survey sites: analyses of these LAI data are in progress and not presented here.

To allow direct comparisons of benthic communities inside the restoration areas with the Florida Keys reefs, the NCRMP dataset was restricted to strata types overlapping M:IR sites and depths less than 12 meters. A majority of the reef habitats within the seven M:IR areas ranged from 0-12 meters depth. Statistical comparisons were conducted between M:IR and NCRMP estimates for each survey year and between years for M:IR and NCRMP. This report focuses on coral populations and benthic community metrics; a separate report can be found for fish population assessments (Blondeau et al., 2025).

Sentence about all data using package (Groves et al., 2025)

2 Summary of Benthic Surveys

In 2022, a total of 584 surveys occurred (Table 1) across 403 sites (Viehman et al., 2023). In 2024, 771 surveys occured across 542 sites (Grove et al., in prep).

Table 1. Still Workshopping. Trying to get it to be in R instead of as a photo but R does NOT like the multi headers

2.1 Benthic Composition

Table 2. Number of benthic cover sites sampled inside and outside M:IR areas in each stratum.
Study Area Strata Name Strat Description 2022 Sample Number 2024 Sample Number
Inside (M:IR) CFK01 Inshore reef, all relief types and depths 8 10
Inside (M:IR) CFK02 Mid-channel patch reef, all relief types and depths 12 12
Inside (M:IR) CFK03 Offshore patch reef, all relief types and depths 7 8
Inside (M:IR) CFK04 Forereef, low relief, shallow (0-6 m) -- 3
Inside (M:IR) CFK05 Forereef, high relief, shallow (0-6 m) 24 33
Inside (M:IR) CFK06 Forereef, low relief, mid-shallow (6-12 m) 4 9
Inside (M:IR) CFK07 Forereef, high relief, mid-shallow (6-12 m) 32 28
Outside (NCRMP) CFK01 Inshore reef, all relief types and depths 10 9
Outside (NCRMP) CFK02 Mid-channel patch reef, all relief types and depths 21 13
Outside (NCRMP) CFK03 Offshore patch reef, all relief types and depths 9 8
Outside (NCRMP) CFK04 Forereef, low relief, shallow (0-6 m) -- 6
Outside (NCRMP) CFK05 Forereef, high relief, shallow (0-6 m) 7 9
Outside (NCRMP) CFK06 Forereef, low relief, mid-shallow (6-12 m) 9 7
Outside (NCRMP) CFK07 Forereef, high relief, mid-shallow (6-12 m) 10 28

2.2 Coral Demography

Table 3. The number of coral demographic sites sampled inside and outside M:IR areas in each stratum (includes DRM data).
Study Area Strata Name Strat Description 2022 Sample Number 2024 Sample Number
Inside (M:IR) CFK01 Inshore reef, all relief types and depths 12 10
Inside (M:IR) CFK02 Mid-channel patch reef, all relief types and depths 16 12
Inside (M:IR) CFK03 Offshore patch reef, all relief types and depths 7 11
Inside (M:IR) CFK04 Forereef, low relief, shallow (0-6 m) -- 4
Inside (M:IR) CFK05 Forereef, high relief, shallow (0-6 m) 25 38
Inside (M:IR) CFK06 Forereef, low relief, mid-shallow (6-12 m) 4 12
Inside (M:IR) CFK07 Forereef, high relief, mid-shallow (6-12 m) 34 34
Outside
(NCRMP + DRM)
CFK01 Inshore reef, all relief types and depths 27 24
Outside
(NCRMP + DRM)
CFK02 Mid-channel patch reef, all relief types and depths 79 109
Outside
(NCRMP + DRM)
CFK03 Offshore patch reef, all relief types and depths 37 42
Outside
(NCRMP + DRM)
CFK04 Forereef, low relief, shallow (0-6 m) 4 31
Outside
(NCRMP + DRM)
CFK05 Forereef, high relief, shallow (0-6 m) 21 45
Outside
(NCRMP + DRM)
CFK06 Forereef, low relief, mid-shallow (6-12 m) 19 33
Outside
(NCRMP + DRM)
CFK07 Forereef, high relief, mid-shallow (6-12 m) 60 61

M:IR selected 10 focal coral species for comparison to NCRMP: Acropora palmata, Acropora cervicornis, Colpophyllia natans, Dendrogyra cylindrus, Dichocoenia stokesii, Diploria labyrinthiformis, Meandrina meandrites, Montastraea cavernosa, Pseudodiploria clivosa, and Pseudodiploria strigosa. The following table summarizes the number of observations across all stratum and survey years of each focal species and identifies the most abundant species encountered.

Table 4. Most Observed Species and Focal M:IR Species Each Year
Species Colonies in 2022 Colonies in 2024
Siderastrea siderea 3,868 5,618
Porites astreoides 2,657 2,132
Stephanocoenia intersepta 1,345 1,534
Agaricia agaricites 884 237
Porites porites 776 558
*Montastraea cavernosa 437 645
Orbicella faveolata 266 237
Orbicella annularis 211 156
Siderastrea radians 182 328
Porites furcata 160 77
Porites divaricata 118 100
*Dichocoenia stokesii 106 137
*Colpophyllia natans 103 76
Solenastrea bournoni 79 113
*Acropora cervicornis 74 13
*Diploria labyrinthiformis 50 65
*Pseudodiploria strigosa 50 46
Eusmilia fastigiata 45 75
*Pseudodiploria clivosa 23 31
*Acropora palmata 14 NA
*Meandrina meandrites 5 11
* indicates M:IR focal species

3 Benthic Community Composition

Temporal trends in benthic cover of functional groups such as coral and macroalgae cover provide information on changes to the benthic community composition over time.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

Figure 2. Cover estimates for main benthic groups inside and outside M:IR areas for 2022 and 2024. A black (+) indicates a significant difference between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance difference between years for the given group (i.e., M:IR or NCRMP). The category ‘Other’ comprises Cyanobacteria, Palythoa, Millepora, Seagrass, Bare Substrate, and other miscellaneous organisms.

4 Coral Demography

Insert more text here. Sentence about surveys designed to produce population estimates of coral species. Metrics for status, trends and restoration effects(?) - density, partial mortality, mean colony size, colony size frequency, and colony size partial mortality. Only focal M:IR species are reported below

The following figures for these metrics are grouped by each focal species. Significant statistical differences are indicated for differences between survey years and between areas (MIR vs. NCRMP) for density, old mortality, and mean colony size.

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

Figure 3. Coral density, old mortality, colony size, and size frequency distribution for focal M:IR species across sample years (2022 and 2024) and survey types (MIR and NCRMP + DRM). A black (+) indicates a significant difference in cover estimates between groups in that survey year (i.e., 2022 or 2024). A colored (*) indicates significance between years for the given group (i.e., M:IR or NCRMP).

4.1 Coral Density

Figure 4. Caption needed here!

4.2 Old Mortality

Figure 5. Caption needed here!

4.3 Coral Size

Figure 6. Caption needed here too!

4.4 Bleaching Estimates

Figure 7. Individual Species’ Observed Bleaching Frequency Outside (NCRMP + DRM) and Inside (M:IR) areas.

4.5 Disease Estimates

Figure 8. Individual Species’ Observed Diseased Frequency Outside (NCRMP + DRM) and Inside (M:IR) areas.

5 Supplemental Information

Point of Contact:
NCRMP Atlantic Benthic Team Lead: Shay Viehman (shay.viehman@noaa.gov)

Data Sources:
National Coral Reef Monitoring Program Florida Benthic (NCRMP)
Florida Fish and Wildlife Conservation Commission’s Disturbance Response Monitoring (DRM)

References

Ault, J. S., Smith, S. G., Luo, J., Grove, L. J., Johnson, M. W., & Blondeau, J. (2021). Refinement of the southern florida reef tract benthic habitat map with habitat use patterns of reef fish species [Dataset]. NOAA National Centers for Environmental Information. https://www.ncei.noaa.gov/archive/accession/0224176
Blondeau, J. B., Groves, J., & Harper, R. (2025). Mission: Iconic reefs RVC analysis. NOAA Coral Reef Conservation Program.
Groves, S., Mateski, J., Krampitz, N., Sturm, A. M., & Viehman, T. S. (2025). NCRMP benthics statistical package in r (website). R package version 1.0.0. https://github.com/MSE-NCCOS-NOAA/NCRMP_benthics
NOAA Coral Reef Conservation Program (CRCP). (2024a). National coral reef monitoring program (NCRMP) benthic community assessment survey field protocols for u.s. Atlantic: Florida, flower garden banks, puerto rico, and u.s. Virgin islands (p. 29). NOAA Coral Reef Conservation Program. https://doi.org/10.25923/e3gf-vk84
NOAA Coral Reef Conservation Program (CRCP). (2024b). National coral reef monitoring program (NCRMP) coral demographics survey field protocols for u.s. Atlantic: Florida, flower garden banks, puerto rico, u.s. Virgin islands (p. 28). NOAA Coral Reef Conservation Program. https://doi.org/10.25923/hgpr-jm80
NOAA Coral Reef Conservation Program (NOAA CRCP). (2022). National coral reef monitoring program (NCRMP) benthic community assessment survey field protocols for u.s. Atlantic: Florida, flower garden banks, puerto rico, and u.s. Virgin islands–2022. NOAA Coral Reef Conservation Program. https://doi.org/10.25923/0708-8333
NOAA Coral Reef Conservation Program [NOAA]. (2022). National coral reef monitoring program (NCRMP) coral demographics survey field protocols for u.s. Atlantic: Florida, flower garden banks, puerto rico, u.s. Virgin islands–2022. NOAA Coral Reef Conservation Program. https://doi.org/10.25923/9a1r-m911
NOAA National Marine Fisheries Service. (2014). Endangered and threatened wildlife and plants: Final listing determinations on proposal to list 66 reef-building coral species and to reclassify elkhorn and staghorn corals. Federal Register, 79(175), 53851–54123.
Viehman, T. S., Grove, J. G., Blondeau, J., Cain, E., Edwards, K. F., Groves, S. H., Krampitz, N., Langwiser, C., Siceloff, L., Swanson, D., Towle, E. K., & Williams, B. (2023). National coral reef monitoring program, biological monitoring summary – florida: 2022 [Technical Memorandum NOS CRCP 48]. NOAA. https://doi.org/10.25923/e6xg-1989